First off, we can rule out Dusknoir's time travel since Ness has Immunity to time paradoxes. Dusknoir's non-corporeality doesn't help either as Ness can still hit intangible foes.
One of Ness' best traits is his incredible healing. He may not have Regenerationn, but Lifeup gamma restores him to full health and is very cheap compared to the amount of Pp he has at level 99. If you restrict Dusknoir to its Gen 4 level up learnset, he has no way to keep up with Ness' healing. Even if you're willing to give Dusknoir access to TMs and tutor moves, the only healing ability he has is Rest, which may fully heal him, but also makes him vulnerable to attack. With Pain Split, Dusknoir could easily keep up, but that is a move that can only be learned via breeding, and if my memory serves me correctly, the Dusknoir in PMD never used it, so it probably shouldn't be considered. (Edit: Just realized that Pain Split is a tutor move in HGSS. Its applicability is still questionable though, so this doesn't really change much)
Another thing to consider is status moves. Dusknoir has Confuse Ray and Will-O-Wisp in its standard set, but these both won't really do anything since Ness can easily use Healing to get rid of them both. Ness on the other hand has Hypnosis to lull Dusknoir to sleep and make it an easy target, and has Flash, which can cause Dusknoir to become confused, lower its accuracy (via crying), and has a pretty good chance (37.5%) to OHKO at the omega level. Dusknoir does have Disable, though it only works on one move at a time.
I vote Ness
